Dear Heidi,

maybe there is a problem with your long.qdec.table.dat file? It is used to create the <fsid>.long.<fs_baseid> file names and obviously that filename is wrong (containing two .long. in it). Make sure that the first column is only the cross sectional id and the second one is the base id, so in your case:
fsid fsid-base
FS_PD002_1.nii FSBASE_002

Also it is not a good idea to have the ".nii" as part of the subject id, as that is a file extension. Next time, when running the cross sectionals, make sure you call the subject "FS_PD002_1" without extension. Could be that this leads to other problems (or it could just work, we'll see).

Best, Martin




On 11/04/2015 08:38 AM, Heidi Foo wrote:
Dear FreeSurfer experts, 

I was running the first stage of analysis of preparing of data - qcache - and I encountered some problems. 

When using this command, long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR, an error message saying:" FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label does not exist!" appears. 

I tried several other ways such as using long_stats_slopes, but I keep receiving error messages similar to the one above. 

Please advice? 

Thank you so much for your kind help! 

Regards, 
Heidi Foo

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu